PyRx - Virtual Screening Tool / News: Recent posts

ANN: Preview Release 0.5

I'm pleased to announce the release of PyRx 0.5, an open source software for Computer-Aided Drug Design. Major changes in this new release are:

* Added Save as Comma-Separated Values (CSV) tool for database tables.
* Added plotting feature for database tables. This feature can be accessed through a toolbar button under Tables tab. By default, it opens up Table Plotting Dialog where a bar plot of Binding Energy versus Ligand (index) is shown. If you have PubChem BioAssay opened using open CVS button, this widget will also check to see if there is Outcome column in that table, and if so, it will color bars corresponding to "Active" compound red and bars corresponding to "Inactive" blue.
* Changed default force field for Open Babel energy minimization from UFF to MMFF94.
* Changed default for maximum number of energy evaluations (generic algorithm parameter in AutoDock) from medium (ga_num_evals = 2500000) to short (ga_num_evals = 250000).
* Added AutoDock PBS job submission progress dialog.
* Fixed a bug that was causing problems when displaying molecular surfaces for docked conformations.
* Added a dialog to select alternate conformation when making macromolecule file (pdbqt) for AutoDock.
* Enabled Enthought's quality agent that can be used to get bug report and comments from a user.
* Added Cancel option for AutoGrid Web Services.
* Implemented flexible residues for AutoDock. This feature can be accesses by selecting residue(s) under Navigator->Molecules and right-clicking on them. Select AutoDock -> Flexible Residues to create _flex folder under Navigator -> AutoDock -> Macromolecules with receptor pdbqt and flex.pdbqt. All docking to this receptor is then done with this flexible residue(s).
* Updated Python to version 2.6 and ETS to 3.4.0.
* The new installers delete previous installation folder, if any, before installing this new version.
Posted by Sarkis Dallakian 2010-03-25

ANN: Preview Release 0.5

I'm pleased to announce the release of PyRx 0.5, an open source software for Computer-Aided Drug Design. Visit http://pyrx.scripps.edu to learn more about PyRx. Major changes in this new release are:

* Added Save as Comma-Separated Values (CSV) tool for database tables.
* Added plotting feature for database tables. This feature can be accessed through a toolbar button under Tables tab. By default, it opens up Table Plotting Dialog where a bar plot of Binding Energy versus Ligand (index) is shown. If you have PubChem BioAssay opened using open CVS button, this widget will also check to see if there is Outcome column in that table, and if so, it will color bars corresponding to "Active" compound red and bars corresponding to "Inactive" blue.
* Changed default force field for Open Babel energy minimization from UFF to MMFF94.
* Changed default for maximum number of energy evaluations (generic algorithm parameter in AutoDock) from medium (ga_num_evals = 2500000) to short (ga_num_evals = 250000).
* Added AutoDock PBS job submission progress dialog.
* Fixed a bug that was causing problems when displaying molecular surfaces for docked conformations.
* Added a dialog to select alternate conformation when making macromolecule file (pdbqt) for AutoDock.
* Enabled Enthought's quality agent that can be used to get bug report and comments from a user.
* Added Cancel option for AutoGrid Web Services.
* Implemented flexible residues for AutoDock. This feature can be accesses by selecting residue(s) under Navigator->Molecules and right-clicking on them. Select AutoDock -> Flexible Residues to create _flex folder under Navigator -> AutoDock -> Macromolecules with receptor pdbqt and flex.pdbqt. All docking to this receptor is then done with this flexible residue(s).
* Updated Python to version 2.6 and ETS to 3.4.0.
* The new installers delete previous installation folder, if any, before installing this new version.
Posted by Sarkis Dallakian 2010-03-25